From 5bd1cc84ebeed7133332e4cf3b25419dec3f124b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Thu, 25 Jul 2024 16:41:27 +0200 Subject: [PATCH 01/12] Update meta.yaml --- recipes/parm/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index cc2b6ed42e026..56a0a833c72bb 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -22,7 +22,8 @@ requirements: run: - python >=3.10.8 - - pytorch + - pytorch=1.13.1 + - pytorch-cuda=11.6 - biopython - numpy >=1.26.0 - pandas From 0a0192cfd218b91f204d2d45e125afdf00f11283 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Thu, 25 Jul 2024 17:58:17 +0200 Subject: [PATCH 02/12] Update meta.yaml --- recipes/parm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 56a0a833c72bb..2ce3801d4145c 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -22,8 +22,8 @@ requirements: run: - python >=3.10.8 - - pytorch=1.13.1 - - pytorch-cuda=11.6 + - pytorch =1.13.1 + - pytorch-cuda =11.6 - biopython - numpy >=1.26.0 - pandas From 3e3091295b4438f7bc4add81e736f7c8ab7d2a2a Mon Sep 17 00:00:00 2001 From: vhfsantos Date: Fri, 26 Jul 2024 10:56:08 +0200 Subject: [PATCH 03/12] update parm --- recipes/parm/meta.yaml | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 2ce3801d4145c..aa582d7e04862 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -21,9 +21,8 @@ requirements: - pip run: - - python >=3.10.8 - - pytorch =1.13.1 - - pytorch-cuda =11.6 + - python + - pytorch-cuda - biopython - numpy >=1.26.0 - pandas @@ -38,9 +37,22 @@ requirements: test: commands: - - parm --help + - parm train --help about: home: https://github.com/vansteensellab/PARM license: https://github.com/vansteensellab/PARM/blob/main/LICENSE summary: promoter activity regulatory model + +extra: + identifiers: + - bioconda: parm + recipe-maintainers: + - vhfsantos + +channels: + - anaconda + - conda-forge + - bioconda + - pytorch + - nvidia From 3e041ebb26c39764d801a4d0b46275c14f3974aa Mon Sep 17 00:00:00 2001 From: vhfsantos Date: Fri, 26 Jul 2024 11:09:05 +0200 Subject: [PATCH 04/12] Update meta.yaml --- recipes/parm/meta.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index aa582d7e04862..942ed9bb7a542 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('parm', max_pin="x.x") }} @@ -44,12 +44,6 @@ about: license: https://github.com/vansteensellab/PARM/blob/main/LICENSE summary: promoter activity regulatory model -extra: - identifiers: - - bioconda: parm - recipe-maintainers: - - vhfsantos - channels: - anaconda - conda-forge From 9a50ccc1df0adf79015b5946f0b09ee9bedb686c Mon Sep 17 00:00:00 2001 From: vhfsantos Date: Fri, 26 Jul 2024 11:40:34 +0200 Subject: [PATCH 05/12] replace torch-cuda with cuda-toolkit --- recipes/parm/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 942ed9bb7a542..9365ff9eb8993 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -22,7 +22,7 @@ requirements: run: - python - - pytorch-cuda + - cuda-toolkit =11.6.1 - biopython - numpy >=1.26.0 - pandas From 27c1f9d9c17b489fbd7e7521e44b363f0ad6fc48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Mon, 29 Jul 2024 15:18:23 +0200 Subject: [PATCH 06/12] Update meta.yaml --- recipes/parm/meta.yaml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 9365ff9eb8993..ad00fa093e6c5 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: noarch: python - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('parm', max_pin="x.x") }} @@ -22,7 +22,6 @@ requirements: run: - python - - cuda-toolkit =11.6.1 - biopython - numpy >=1.26.0 - pandas @@ -47,6 +46,4 @@ about: channels: - anaconda - conda-forge - - bioconda - - pytorch - - nvidia + - bioconda From d41dd96c55fc89be5ea2d2c978d509a05bcd6608 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Mon, 29 Jul 2024 15:43:44 +0200 Subject: [PATCH 07/12] Update meta.yaml --- recipes/parm/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index ad00fa093e6c5..b3b7006291fb9 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -22,6 +22,7 @@ requirements: run: - python + - pytorch - biopython - numpy >=1.26.0 - pandas @@ -47,3 +48,4 @@ channels: - anaconda - conda-forge - bioconda + - pytorch From 59ef6d12338ad2c125becfacec5bdaf403108948 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Wed, 31 Jul 2024 11:02:42 +0200 Subject: [PATCH 08/12] Remove channels from recipe --- recipes/parm/meta.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index b3b7006291fb9..822aace9f1dbc 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -43,9 +43,3 @@ about: home: https://github.com/vansteensellab/PARM license: https://github.com/vansteensellab/PARM/blob/main/LICENSE summary: promoter activity regulatory model - -channels: - - anaconda - - conda-forge - - bioconda - - pytorch From 5d4d14f11adca7dfccf733fd4f7e89cc68ae52df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Wed, 31 Jul 2024 13:16:43 +0200 Subject: [PATCH 09/12] Update meta.yaml --- recipes/parm/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 822aace9f1dbc..43aa89fff9051 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -19,6 +19,7 @@ requirements: host: - python - pip + - setuptools run: - python From ae0608c9048e793c376f1e548ba1d1f5f80bd50b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Tue, 19 Nov 2024 10:51:33 +0100 Subject: [PATCH 10/12] Update v0.0.7 --- recipes/parm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 43aa89fff9051..076b932b9518a 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.0.6" %} -{% set sha256 = "58853578e42e76ecb9e609cb9b292fa979ae5a999d28126f3c43ac0e986f44a5" %} +{% set version = "0.0.7" %} +{% set sha256 = "91d7acc85aac2ef18d2effc2624f0c09160f8077" %} package: name: parm From b483a249dd653227bc02040e21c08c34ff30c3cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Tue, 19 Nov 2024 10:57:00 +0100 Subject: [PATCH 11/12] Update meta.yaml --- recipes/parm/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 076b932b9518a..886051a2cc242 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: noarch: python - number: 2 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('parm', max_pin="x.x") }} From 084c6ffc68757146462ea971827879d102a19fa2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?= Date: Tue, 19 Nov 2024 11:07:13 +0100 Subject: [PATCH 12/12] Update meta.yaml --- recipes/parm/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml index 886051a2cc242..f5ad767d5bbf3 100644 --- a/recipes/parm/meta.yaml +++ b/recipes/parm/meta.yaml @@ -1,5 +1,5 @@ {% set version = "0.0.7" %} -{% set sha256 = "91d7acc85aac2ef18d2effc2624f0c09160f8077" %} +{% set sha256 = "5f6a94d86ba026ac816eae8e27fbec00d2b25a7c5f5729101474f758d7dcbcc9" %} package: name: parm